Laser scanning confocal microscopes have the ability to penetrate beneath the surface of a specimen to obtain slices of imaging data. These slices or sections can be taken at specific depths in the specimen and then can be recombined to form a three dimensional image of the examined section. In order to be viewed by the laser scanning confocal microscope, the section of the specimen being examined must be auto-fluorescent or be stained with fluorescent dyes.
Unfortunately, control of laser scanning confocal microscopes has been fairly difficult and rigid. As a result, an operator of a laser scanning confocal microscope must spend a great deal of time and effort to modify the operation of a laser scanning confocal microscope for particular application. Additionally, there have been some deficiencies in controlling the timing of different operations within the laser scanning confocal microscope.